User: tobias.kockmann

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Posts by tobias.kockmann

<prev • 27 results • page 1 of 3 • next >
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Comment: C: how to transform a list of IRanges into a RangesList instance
... Hi Martin, I am having a bit of a problem using as(..., "RangesList") in the context of my package. I always get the error that the appropriate method is not found in the context of testthat(...). How would you handle this? Calling the RangesList() constructor directly instead of as() -> coerce( ...
written 2.5 years ago by tobias.kockmann20
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Comment: C: how to transform a list of IRanges into a RangesList instance
... I tried to use as(..., "IRangesList") and got: Error in as(y, "IRangesList") : no method or default for coercing "list" to "IRangesList" Is there a reason why one can not coerce a list to a IRangesList? What is more specific about IRangesList objects? ...
written 2.6 years ago by tobias.kockmann20
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findOverlaps - how to get adjacent ranges?
... Hi there, I am trying to locate a function that finds pairs of adjacent ranges - ranges where the end of range A is exactly start-1 of range B. Example with 3 ranges: AAAAABBBBBCCCCC pair 1 AAAAA BBBBB pair 2 BBBBB CCCCC I thought that would be possible using findOverlaps() or findOverlapPairs( ...
iranges findoverlaps written 2.6 years ago by tobias.kockmann20 • updated 2.6 years ago by Michael Lawrence11k
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX Martin! A general question: I am starting to develop a package for dealing with peptide mapping data (data coming from a bottom-up proteomics experiment) and I think the Biostrings and IRanges package could be the basis for this, but I am having trouble to get an overview what functionality is a ...
written 2.7 years ago by tobias.kockmann20
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Comment: C: how to transform a list of IRanges into a RangesList instance
... THX! > real.rl <- as(rl, "RangesList") > class(real.rl) [1] "SimpleRangesList" attr(,"package") [1] "IRanges" Where is that function documented? ...
written 2.7 years ago by tobias.kockmann20
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how to transform a list of IRanges into a RangesList instance
... Dear bioC support, I have constructed a list of IRanges named rl: > class(rl) [1] "list" > class(rl[[1]]) [1] "IRanges" attr(,"package") [1] "IRanges" Now I realized that there is already a RangesList class in the IRanges package that I could use instead of the "primitive" list. Problem: I ...
rangeslist-class {iranges} written 2.7 years ago by tobias.kockmann20 • updated 2.7 years ago by James W. MacDonald51k
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Comment: C: Ranges on AAStrings
... I found two exceptions. findOverlaps() and countOverlaps() work directly on the Views object if queried against itself (within proteins for a AAString subject): hits <- findOverlaps(query = v1, maxgap = 1, drop.self=TRUE, drop.redundant=TRUE) c <- countOverlaps(query = v1, maxgap = 1, drop. ...
written 2.7 years ago by tobias.kockmann20
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Comment: C: Ranges on AAStrings
... True thought! ...
written 2.7 years ago by tobias.kockmann20
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Ranges on AAStrings
... Hi BioC, can anyone help me with the following: I mapped a set of peptides (short AA sequences) to a set of proteins using exact string matching. Now, I would like to compare the locations of the mapped peptide to each other, in order to find peptides that locate next to one another. To me this pr ...
biostrings aastring views written 2.7 years ago by tobias.kockmann20
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Hi Herve, hmmm...I looked at the size of the list of MIndex objects returned and got this: > object.size(m[[1]]) 9458832 bytes In total the list contains 10 of these MIndex objects, so the list of MIndex objects has a total memory footprint of 90 Mb! The corresponding list-of-list structure ...
written 2.8 years ago by tobias.kockmann20

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